Document how to run pyAFQ through qsiprep

[arokem]

We (and by that. I really mean I) might need a step-by-step on how to set up the config and run this.

[36000]

This is a good place to start: https://qsiprep.readthedocs.io/en/latest/reconstruction.html However, until the next release, pyAFQ is only on master, so here is the corresponding rst on master: https://github.com/PennLINC/qsiprep/blob/master/docs/reconstruction.rst This JSON is the one you can edit, though I think it is already ready to go for most purposes: https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/pipelines/pyafq_input_trk.json

[36000]

IE, the command is:

$ qsiprep-docker \
    /path/to/bids /where/my/reconstructed/data/goes participant \
    --recon_input /output/from/qsiprep \
    --recon_spec pyafq_input_trk.json \
    --fs-license-file /path/to/license.txt

[arokem]

Thanks! That's super helpful for me, but I also think that it would be good to add something like this to our docs (maybe we'll need to wait for another qsiprep release), because someone visiting our documentation wouldn't know that they can do this.

[arokem]

A couple of questions to follow up:

1. Are we supposed to run qsiprep just for preprocessing first, before running this?
2. Is there some way to run this as a docker call? That is, starting with docker run. This in particular is for systems where I have to run everything from docker and can't install anything outside of docker. Presumably, I can't install qsiprep-docker inside of a docker container because it also needs docker.